convert_bed_to_matrix: convert the bed file to matrix file for the next analysis
In HBP: Hi-C BED File Analysis Pipeline

convert the bed file to matrix file for the next analysis

`bedfile`
`bin`
`chrom_list`
`tot_size`
`bed_window`

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (bedfile, bin = 2000, chrom_list = "chr2L", tot_size = 0,
    bed_window = 2000)
{
    if (tot_size == 0) {
        print("please input tot_size")
    }
    else {
        cmap = matrix(data = 0, nrow = tot_size, ncol = 1)
        sec = NULL
        for (j in 1:length(chrom_list)) {
            sec = rbind(sec, bedfile[bedfile$chr == chrom_list[j],
                ])
        }
        ordereduniques = sec
        count = 0
        for (i in 1:dim(ordereduniques)[1]) {
            st = (ceiling(ordereduniques[i, 2]/bin))
            ed = (ceiling(ordereduniques[i, 3]/bin))
            st1 = (ceiling((ordereduniques[i, 2] - bed_window)/bin))
            ed1 = (ceiling((ordereduniques[i, 3] + bed_window)/bin))
            if (st < 1) {
                st = 1
            }
            if (st1 < 1) {
                st1 = 1
            }
            if (ed < 1) {
                ed = 1
            }
            if (ed1 < 1) {
                ed1 = 1
            }
            if (st > tot_size) {
                st = tot_size
            }
            if (st1 > tot_size) {
                st1 = tot_size
            }
            if (ed > tot_size) {
                ed = tot_size
            }
            if (ed1 > tot_size) {
                ed1 = tot_size
            }
            if (st != ed) {
                cmap[st, 1] = cmap[st, 1] + 1
                count = count + 1
                cmap[ed, 1] = cmap[ed, 1] + 1
                count = count + 1
                if (st1 != st) {
                  cmap[st1, 1] = cmap[st1, 1] + 1
                  count = count + 1
                }
                if (ed1 != ed) {
                  cmap[ed1, 1] = cmap[ed1, 1] + 1
                  count = count + 1
                }
            }
            else {
                cmap[ed, 1] = cmap[ed, 1] + 1
                count = count + 1
                if (st1 != st) {
                  cmap[st1, 1] = cmap[st1, 1] + 1
                  count = count + 1
                }
                if (ed1 != ed) {
                  cmap[ed1, 1] = cmap[ed1, 1] + 1
                  count = count + 1
                }
            }
        }
    }
    cat(sprintf("Mapped Fragments: %s\n", count))
    return(cmap)
  }